The role of water dynamics in mediating protein‐DNA interactions (549.4)

Abstract

The role of hydration water on protein and DNA surfaces is fundamental to their interaction and processes, yet experimentally challenging to study. We recently applied a novel Overhauser dynamic nuclear polarization‐enhanced NMR method to the study of biological hydration water which provides unprecedented insights into ps to sub‐ns water dynamics within 5‐10 Angstrom of molecular surfaces: waters loosely associated with DNA have surprisingly high degrees of mobility, nearly unperturbed, while waters surrounding protein surfaces are significantly fortified, compared to the dynamics of bulk water. Here we investigated how water mobility contributes to the site location mechanisms of several DNA binding proteins. Dimethyl sulfoxide increases this water mobility on molecular surfaces (DNA or protein) and is predicted to increase the site location efficiency of proteins that rely extensively on a sliding mechanism; we confirmed this to be the case with EcoRI endonuclease when adding 1% DMSO. In contrast, glycerol is predicted to have a retarding (or sometimes neutral) effect on surface water mobility and thus sliding translocation kinetics, which we again confirm to be the case with EcoRI endonuclease when adding 1% glycerol. In contrast, the translocation efficiency of DNA adenine methyltransferase (Dam) that does not rely extensively on sliding is not altered with either osmolyte addition. The observed effects on processivity have been corrected for minor changes in catalytic efficiency in the presence of osmolytes. Our results reveal that water’s fast moving properties around DNA are important for protein‐DNA interactions and in particular, the translocation along the double helix, whose efficiency can be slowed or enhanced when the water barrier on the DNA or protein surfaces is strengthened or weakened by the addition of glycerol or DMSO.